Tag Archives: diatoms

Four Diatom Problems

Zheng2015 Late Fig 43782_MediaPlayer_63659_06222015_195640

(By Michael Zheng, 2015)

TEM (Transmission Electron Microscopy) is a rare skill. I did a little when I wrote:
  • Bender, R., Bellman, S.H. and Gordon, R. (1970) ART and the ribosome: a preliminary report on the three-dimensional structure of individual ribosomes determined by an Algebraic Reconstruction Technique. J. Theor. Biol. 29, 483-488.

and learned to appreciate those who do it well.

There are 4 diatom problems I’d like to see solved, for which TEM may prove critical:
  1. What is the pathway (literally, not just biochemically) by which oil droplets are formed, coalesced, accumulated, passed out of the plastids, occupy huge volumes inside the diatom, and via milking or spontaneously get outside the diatom? Such knowledge may prove critical to biofuel production.
  2. Triangular Archaea and triangular centric diatoms sometimes have square (90deg) corners instead of the “expected” 60deg. This suggests some structure, something like a centriole, in those corners. What is there, if anything?
  3. Is there any correlation between the 3D array of microtubules and microfilaments and the shape of a diatom valve? If yes, can we observe how the relationship changes during valve morphogenesis?
  4. In motile pennate diatoms, what is the pathway by which raphe fibrils are formed and exit the cell membrane? Once out, are they attached to the membrane or not, while they traverse the raphe?
Regarding #2: While most plants do not have centrosomes, diatoms do, if not proper centrioles:

Shaped droplets, diatoms and the origin of life

A remarkable paper appeared online 09 December 2015:

The authors, materials scientists from Bulgaria and the UK, mused out loud that their discovery that cooled oil droplets become polygonal had something to do with the morphogenesis of living creatures, but didn’t know which ones. I immediately started writing “On polygonal drops and centric diatoms” followed shortly by “The tensegrity origin of life via shaped droplets as protocells”, and some of the authors of “Self-shaping of oil droplets” are joining us as co-authors.

I had long been puzzling over the uncanny, nearly perfect symmetry of some centric diatoms, which I demonstrated by rotating a digital image of a diatom with n sectors by 360/n degrees and subtracting the images, in:

  • Sterrenburg, F.A.S., R. Gordon, M.A. Tiffany & S.S. Nagy (2007). Diatoms: living in a constructal environment. In: Algae and Cyanobacteria in Extreme Environments. Series: Cellular Origin, Life in Extreme Habitats and Astrobiology, Vol. 11. Ed.: J. Seckbach. Dordrecht, The Netherlands, Springer: 141-172.

Here’s a less perfect example than those used in that paper, the diatom Triceratium favus with n = 3, so the rotation is 360/3 = 120o (with kind permission of Stephen S. Nagy of Montana Diatoms):


The subtraction image on the right is black where the match is best. The two published examples, with n = 5 and 11, came out almost totally black. You can try this yourself with any front-on image of a diatom you can find on the Internet, if you have software that allows rotation by any angle. For example, try Word: Format Picture: Size: Rotate and scale, after trimming the picture so that the center of the diatom is in the center of the image. I’d like to see what you get. Please send the original, rotated and difference images to me at: DickGordonCan@gmail.com, along with the exact source of the diatom image. Anyone mathematically inclined (and these diatoms instantiate a rotation group) may wish to write a computer program to quantify the degree of symmetry by coding some of the math in:

We in polar climes are all aware of the beautiful, generally hexagonal symmetry of snowflakes, which has it explanation in the crystalline stacking of water molecules in ice. Some can approach triangular, although they are hexagons with edges of different lengths:

Libbrecht2016 triangular.jpg

This is from:

Libbrecht, K.G. (2016). Guide to Snowflakes: Triangular Crystals.

with kind permission of Kenneth G. Libbrecht. More pointy triangular snowflakes may be seen at:

Bentley, W.A. & W.J. Humphreys (1931). Snow Crystals,  McGraw-Hill. (reprinted by Dover Press in 2003).

But diatom shells are not crystalline at all. They are made of amorphous silica, which at higher temperatures would be molten glass. They are frozen in the glassy state. Are diatoms real life cases of the liquid metal robot T-1000 in the movie Terminator 2? That puzzle is why diatom symmetry is uncanny.

So we start the New Year with a newly discovered phenomenon: oil drops that “should” be mere spherical blobs looking like diatoms. I’ll just show one oil triangle here (with permission of Nature Publishing Group), though the polygons go up to 11 sides:


Denkov&2015 Fig2b triangle.jpg

How can a liquid have sharp points like that?

Connections rattled in my brain. Denkov et al. suggest that the oil molecules line up at the perimeter, forming plastic-like bundles as cooling proceeds. Those bundles could be stiff, and prevent the drop from curving due to its surface tension. But then stiff rods confined by tension means that shaped droplets are tensegrity structures. But this is precisely what Steve Levin and I were complaining about the presentations at the origin of life conference we attended together last November: protocells, the blobs that supposedly led to life, had no postulated structure. Two problems solved at once! Diatoms and protocells are and might have been tensegrity shaped droplets. Martin Hanczyc’s oil droplet protocells might be polygonal under some conditions, and Vadim Annekov’s molecular dynamics simulations of diatom shell morphogenesis interacting with cytokeleton (in progress) may be enhanced. Not quite as good as the kids’ book “Seven in One Blow“, but a very satisfying pair of results.

And by the way, this is why theoretical biologists should be regarded as highly as theoretical physicists, although in general we don’t get no respect.

Diatom Motility – Explosive Breakthrough in Understanding


There are several models of how diatom motility works:

Snail-like movement (proposed by Christian Gottfried Ehrenberg in 1838)

Jet engine like motion using a form of jet propulsion (proposed by Carl von Nägeli in 1849, modified by C.Th. von Siebold in 1853), long before the jet engine was invented!

Rowing model (proposed by J. Hogg in 1855)

Rocket ship model: O. Bütschli (1892) and Robert Lauterborn (1896) proposed that a sticky jelly-like substance, extruded quickly in fine threads at the nodules of the raphes, propels the cells by mechanical recoil.

Extroproplasm streaming model think of a tank tread (proposed by Otto Müller in 1893)

And then there is capillarity (Flame of Life) model: Slide24


A new competing model by Lesley Edgar and Jeremy Pickett-Heaps (1983) proposes that the raphe fibers are passively carried by myosin motor molecules.

The problem of diatom motility is still unsolved.

Lesley Ann Edgar (1955-2006) analyzed movie films of motile diatoms at 10 frames per second and noted erratic accelerations to 100 µm/sec2 (see Edgar, L.A. (1979). Diatom locomotion: computer assisted analysis of cine film. Br. Phycol. J. 14, 83-101.)

  • “It is possible that such a strand is secreted in short units corresponding to release of individual loads of locomotor material from within cytoplasmic vesicles through the plasmalemma, so that locomotion would occur in a series of steps” (Edgar, L.A. (1979). Diatom locomotion: computer assisted analysis of cine film. Br. Phycol. J. 14, 83-101.)

Hm….very interesting result. So we (working with Can Sabuncu and Ali Beskok at Southern Methodist University) followed up, and got the same result, even though our camera is nearly 1000 times faster:


We may be seeing very high speed forward and backwards movement. So maybe the rocket propulsion model is right: strands of mucilage are extruded along the raphe. They hydrate on contact with water exiting the raphe in chemical explosions. These repeated explosions move the diatom along in spurts. The mucilage is left behind as the sticky “diatom trail”. Its elasticity sometimes pulls the diatom backwards as the connection with the trail is stretched and breaks.

Is this correct? We need more research. Our next plan includes computer simulation:Slide36

This blog is a summary version of:

History and future of understanding the mechanism of diatom motility
September 7-12, 2015

Richard Gordon

Gulf Specimen Aquarium & Marine Laboratory, Panacea, Florida, USA

Ali Beskok & A. Can Sabuncu

Department of Mechanical Engineering

If you would like a copy of the full presentation, please send us a message.

Diatoms are forever.


Centric Diatom (Mary Ann Tiffany)

On Thursday last week Dick was giving a seminar to a group of Russian scientists in Irkutsk on Lake Baikal via Skype. The people there were all familiar with diatoms so before I report on his presentation, I thought I would give some background on diatoms.

Diatoms are unicellular, eukaryotic, photosynthetic algae that are found in aquatic environments. Diatoms have enormous ecological importance on this planet and display a diversity of patterns and structures at the nano- to millimetre scale.

Diatoms are microscopic (2 µm to 4 mm), and species are classified mostly by the shapes and patterns of their hard silica parts. There are 􏰀250 living diatom genera with more than 200 000 estimated species classified by their unique morphologies. The silica (glass) shell, or ‘frustule’, consists of two overlapping valves joined with silica girdle bands, much like a Petri dish. There are two major groups that are separated based on valve symmetry. The pennate diatoms are elongate, usually with bilateral symmetry. Centric diatoms have radial symmetry. The pennates are placed into two classes depending on whether or not they have slits in the valves called raphes. These slits are involved in gliding motility. Dick has been studying diatom motility for most of his adult life and the above is adapted from his review article “The Glass Menagerie: diatoms for novel applications in nanotechnology”


Pennate diatom without a raphe (Mary Ann Tiffany)

Electron Image 16

Pennate diatom with two raphe slits (Mary Ann Tiffany)

Electron Image 17

Close up of a raphe, which goes clear through the shell (Mary Ann Tiffany)

Gardeners are familiar diatomaceous earth which is mostly diatom shells. You are most likely familiar with diatoms for their killer aspect. Diatoms are what gives rocks in running water that lovely slick coating that makes falling in rivers and creeks so easy. During a trip to Yellowstone, we saw a man wading across the rocky bottom of a fast moving small river about 10 meters back from the edge of a five story waterfall. We left before we were forced to to witness the diatoms killing this poor fellow in front of his wife and children. We later reported this to a ranger who sighed deeply and said “Yellowstone is the Olympics of the Darwin Awards. Too bad this guy has already reproduced.”

You can read more about diatoms in a great Wikipedia article. In the meantime here are a couple more of Mary Ann Tiffany’s wonderful images which she has so graciously given us permission to share. Diatoms Are Forever is the title of a book we are working on with a few diatomist colleagues.

Electron Image 41HalfMoonBayht600 Electron Image 52